Tapestry Configuration file - galizia-lab/pyview GitHub Wiki

A tapestry configuration file is a YAML file with a specific format. Here is an example:

# entries 'animal' and 'measus' mandatory for the first row
row1: # row name can be arbitrary, but cannot be repeated

  # animal whose data will be used
  animal: animal1

  # values from the column "Measu" of the measurement list for this animal
  measus: [1, 3, 5, 7]

  # flags to be set before creating overviews
  flags:
    CTV_Method: 22
    CTV_firstframe: 25
    CTV_lastframe: 30
    SO_individualScale: 2

  # overviews are create in compressed PNG format by default. Here you can specify whether uncompressed TIFs should
  # be additionally created
  extra_formats: [tif]

  # whether movies corresponding to the overviews are to be created
  corresponding_movies: False

  # values of all "SO_..." flags above will be used to update analogous "mv_..." flags
  # if any additional flags need to be set before creating movies, they can be specified here
  extra_movie_flags:
    mv_ygap: 30
    mv_xgap: 30
    mv_exportFormat: libx264

# all values missing in this row will be taken from previous row

row2: # row name can be arbitrary, but cannot be repeated
  measus: [2, 4, 6, 8]
row3: # row name can be arbitrary, but cannot be repeated
  measus: [5, 5, 5, 5]

Notes:

• The name of each row, i.e., "row1", "row2" and "row3" in the above example, can be arbitrary text.
• For the first row, an animal and a list of measus must be specified
• For all other rows, one or more of "animal", "measus" and "flags" can be specified. If one of these is not specified, the values from the previous row is used.
• Essentially, for each row, a different animal, a different set of measus and a different set of flags can be specified. Although, it is not necessary to specify all three. At least one is required.
• All overviews of a tapestry are saved as compressed PNG files. The entry "extra_formats: [tif]" specifies that overviews must be additionally saved as uncompressed TIF files.
• Movies corresponding to overviews can be created by setting the entry "corresponding_movies" to True. Values of all "SO_..." flags above will be used to update analogous "mv_..." flags. If any additional flags need to be set before creating movies, they can be specified using "extra_movie_flags".
• Important: Specify the "extra_format" entry only when needed. Each tiff file can be a few hundreds of kB, but when generating many tapestries, it can add up and lead to a lot of waste of disk space. The same goes for movies.